| %>% |
Man page
|
| .alias_row_lengths_from_sizes |
Source code
|
| .append_tracks_to_genome_info |
Source code
|
| .assign_target_chroms_per_row |
Source code
|
| .build_alias_rev_index |
Source code
|
| .build_model_from_gsm |
Source code
|
| .build_ncbi_rename_map |
Source code
|
| .build_seq |
Source code
|
| .build_seq_local |
Source code
|
| .build_seq_manual |
Source code
|
| .build_seq_ncbi |
Source code
|
| .build_seq_s3 |
Source code
|
| .build_seq_ucsc |
Source code
|
| .build_seq_ucsc_hub |
Source code
|
| .builtin_registry_path |
Source code
|
| .canonical_coverage |
Source code
|
| .cell_merge_empty_result |
Source code
|
| .cell_merge_normalize |
Source code
|
| .cell_merge_sample_bin_maps |
Source code
|
| .chrom_alias_lookup |
Source code
|
| .cleanup_empty_dirs |
Source code
|
| .coerce_pssm_matrix |
Source code
|
| .coerce_score_thresh |
Source code
|
| .compute_chrom_aliases |
Source code
|
| .compute_flat_indices |
Source code
|
| .coverage_gate |
Source code
|
| .create_deferred_2d |
Source code
|
| .dedup_motif_ids |
Source code
|
| .detect_alias_column |
Source code
|
| .detect_arch |
Source code
|
| .diagnose_unmapped_chroms |
Source code
|
| .download_to |
Source code
|
| .ensure_filter_compiled |
Source code
|
| .fetch_with_optional_gunzip |
Source code
|
| .find_project_misha_yaml |
Source code
|
| .gcall |
Source code
|
| .gcall_noninteractive |
Source code
|
| .gcheck_write_permission |
Source code
|
| .gcheckroot |
Source code
|
| .gchroms |
Source code
|
| .gcluster.running.jobs |
Source code
|
| .gconfirmtrackcreate |
Source code
|
| .gdata_table_available |
Source code
|
| .gdb.add_intervals.set |
Source code
|
| .gdb.add_track |
Source code
|
| .gdb.apply_collisions |
Source code
|
| .gdb.cache_clear_dirty |
Source code
|
| .gdb.cache_dirty_path |
Source code
|
| .gdb.cache_is_dirty |
Source code
|
| .gdb.cache_mark_dirty |
Source code
|
| .gdb.cache_path |
Source code
|
| .gdb.cache_update_lists |
Source code
|
| .gdb.cache_write_lists |
Source code
|
| .gdb.chrom_names_at |
Source code
|
| .gdb.clear_all_dir_caches |
Source code
|
| .gdb.clear_scan_cache |
Source code
|
| .gdb.convert_attrs |
Source code
|
| .gdb.convert_to_indexed.genome |
Source code
|
| .gdb.convert_to_indexed.get_confirmation |
Source code
|
| .gdb.convert_to_indexed.intervals |
Source code
|
| .gdb.convert_to_indexed.parallel_apply |
Source code
|
| .gdb.convert_to_indexed.resolve_threads |
Source code
|
| .gdb.convert_to_indexed.tracks |
Source code
|
| .gdb.convert_to_indexed.validate_and_setup |
Source code
|
| .gdb.convert_tracks |
Source code
|
| .gdb.ensure_dataset_maps |
Source code
|
| .gdb.find_resource_dbs |
Source code
|
| .gdb.host_tag |
Source code
|
| .gdb.invalidate_dir_cache |
Source code
|
| .gdb.is_indexed |
Source code
|
| .gdb.is_indexed_at |
Source code
|
| .gdb.normalize_cache_list |
Source code
|
| .gdb.resolve_db_for_path |
Source code
|
| .gdb.resolve_track_db |
Source code
|
| .gdb.resource_dbs_impl |
Source code
|
| .gdb.rm_intervals.set |
Source code
|
| .gdb.rm_track |
Source code
|
| .gdb.scan_db_cached |
Source code
|
| .gdb.scan_db_fast |
Source code
|
| .gdb.scan_intervals |
Source code
|
| .gdb.scan_tracks |
Source code
|
| .gdb.staging_name |
Source code
|
| .gdb.staging_owner_gone |
Source code
|
| .gdb.trash |
Source code
|
| .gdb.trash_sweep_old |
Source code
|
| .gdb.validate_resources |
Source code
|
| .gdir.cd |
Source code
|
| .generate_2d_on_demand |
Source code
|
| .gexpr2str |
Source code
|
| .gextract_track_parallel |
Man page
Source code
|
| .gff3_to_genepred_cache_dir |
Source code
|
| .gff3_to_genepred_cache_path |
Source code
|
| .gff3_to_genepred_path |
Source code
|
| .gff3_to_genepred_resolve_or_install |
Source code
|
| .gfindtrackinpath |
Source code
|
| .ggetOption |
Source code
|
| .gintervals |
Source code
|
| .gintervals.2d.load_df |
Source code
|
| .gintervals.apply |
Source code
|
| .gintervals.attr_check_writable |
Source code
|
| .gintervals.attr_path |
Source code
|
| .gintervals.attr_read |
Source code
|
| .gintervals.attr_write |
Source code
|
| .gintervals.big.is1d |
Source code
|
| .gintervals.big.is2d |
Source code
|
| .gintervals.big.meta |
Source code
|
| .gintervals.big.save |
Source code
|
| .gintervals.big.save_meta |
Source code
|
| .gintervals.big2small |
Source code
|
| .gintervals.check_new_set |
Source code
|
| .gintervals.is1d |
Source code
|
| .gintervals.is2d |
Source code
|
| .gintervals.is_bigset |
Source code
|
| .gintervals.is_indexed_bigset |
Source code
|
| .gintervals.load |
Source code
|
| .gintervals.load_ext |
Source code
|
| .gintervals.load_file |
Source code
|
| .gintervals.loadable |
Source code
|
| .gintervals.needs_bigset |
Source code
|
| .gintervals.normalize_for_save |
Source code
|
| .gintervals.save_file |
Source code
|
| .gintervals.save_set_or_return |
Source code
|
| .gintervals.small2big |
Source code
|
| .gintervals_db_path |
Source code
|
| .gis_gzip_file |
Source code
|
| .giterator |
Source code
|
| .glifetime_counters |
Source code
|
| .gmultitasking_strategy |
Man page
Source code
|
| .gnormalize_chrom_names |
Source code
|
| .gparse_strand_vec |
Source code
|
| .gpath_is_within |
Source code
|
| .graise_diagnostics |
Source code
|
| .grbind |
Source code
|
| .gread_bed_table |
Source code
|
| .gread_table_filtered |
Source code
|
| .gseq.import |
Source code
|
| .gseq.import_multifasta |
Source code
|
| .gslice |
Source code
|
| .gsort_intervals_df |
Source code
|
| .gsynth_build_log_p |
Source code
|
| .gsynth_process_parallel |
Source code
|
| .gsynth_resolve_prior_arg |
Source code
|
| .gtake_pending_diagnostics |
Source code
|
| .gtf_to_genepred_cache_path |
Source code
|
| .gtf_to_genepred_path |
Source code
|
| .gtf_to_genepred_resolve_or_install |
Source code
|
| .gtrack.array.get_colnames |
Source code
|
| .gtrack.array.set_colnames |
Source code
|
| .gtrack.attr.import |
Source code
|
| .gtrack.attr.set |
Source code
|
| .gtrack.copy.match_chrom_alias |
Source code
|
| .gtrack.copy.one |
Source code
|
| .gtrack.copy.pipeline |
Source code
|
| .gtrack.copy.raw_dir |
Source code
|
| .gtrack.copy.resolve_dest_db |
Source code
|
| .gtrack.create_atomic |
Source code
|
| .gtrack.create_test_computer2d |
Source code
|
| .gtrack.pack_per_chrom_to_indexed |
Source code
|
| .gtrack.prepare.pvals |
Source code
|
| .gtrack.split_indexed_to_per_chrom |
Source code
|
| .gtrack.var.exists |
Source code
|
| .gtrack.var.get |
Source code
|
| .gtrack.var.set |
Source code
|
| .gtrack_db_path |
Source code
|
| .gtrack_is_bed_path |
Source code
|
| .gtrack_read_bed |
Source code
|
| .gtrack_set_created_attrs |
Source code
|
| .gunzip_to_file |
Source code
|
| .gunzip_to_tempfile |
Source code
|
| .gverify_max_data_size |
Source code
|
| .gvtrack |
Source code
|
| .gvtrack.get |
Source code
|
| .gvtrack.set |
Source code
|
| .gwith_umask |
Source code
|
| .heal_ucsc_tsv_escapes |
Source code
|
| .hub_fetch_assets |
Source code
|
| .hub_list_dir |
Source code
|
| .hub_list_dir_parse |
Source code
|
| .hub_preflight_coverage |
Source code
|
| .hub_url_for |
Source code
|
| .install_cgi_set |
Source code
|
| .install_cytoband_set |
Source code
|
| .install_genes_set |
Source code
|
| .install_gff3_converter |
Source code
|
| .install_gtf_converter |
Source code
|
| .install_intervals_summary |
Source code
|
| .install_rmsk_set |
Source code
|
| .intervals_dir |
Source code
|
| .is_2d_deferred |
Source code
|
| .is_bam_file |
Source code
|
| .is_per_chromosome_db |
Source code
|
| .length_match_fill |
Source code
|
| .length_match_override |
Source code
|
| .load_gsm_dir |
Source code
|
| .load_gsm_zip |
Source code
|
| .make_filter_key |
Source code
|
| .manual_fetch_assets |
Source code
|
| .materialize_chrom_alias_env |
Source code
|
| .merge_assembly_report_into_alias |
Source code
|
| .merge_chrom_aliases_tsv |
Source code
|
| .misha |
Man page
|
| .misha_env |
Source code
|
| .name_match_override |
Source code
|
| .ncbi_dataset_report |
Source code
|
| .ncbi_datasets_zip_url |
Source code
|
| .ncbi_fetch_assets |
Source code
|
| .ncbi_ftp_assembly_dir |
Source code
|
| .ncbi_ftp_assembly_name_from_dir |
Source code
|
| .ncbi_parse_annotation_info |
Source code
|
| .ncbi_resolve_sets_with_preflight |
Source code
|
| .ncbi_seqrep_to_alias_df |
Source code
|
| .ncbi_suggest_annotated_alternative |
Source code
|
| .ncbi_to_ucsc_name |
Source code
|
| .normalize_bounds |
Source code
|
| .normalize_recipe |
Source code
|
| .normalize_report_colname |
Source code
|
| .normalize_ucsc_genepred |
Source code
|
| .normalize_ucsc_tsv |
Source code
|
| .onAttach |
Source code
|
| .onDetach |
Source code
|
| .onLoad |
Source code
|
| .onUnload |
Source code
|
| .parse_genome_registry |
Source code
|
| .parse_jaspar_header |
Source code
|
| .parse_jaspar_simple |
Source code
|
| .parse_meme_key |
Source code
|
| .parse_ncbi_sequence_report |
Source code
|
| .parse_rm_out |
Source code
|
| .parse_ucsc_assembly_report |
Source code
|
| .parse_ucsc_chromalias |
Source code
|
| .parse_ucsc_cpg_island |
Source code
|
| .parse_ucsc_cytoband |
Source code
|
| .parse_ucsc_rmsk |
Source code
|
| .pick_gtf |
Source code
|
| .prompt_yes_no |
Source code
|
| .read_fasta_headers |
Source code
|
| .refresh_chrom_alias_env |
Source code
|
| .rename_fasta_headers |
Source code
|
| .rename_gff3_seqids |
Source code
|
| .renormalize_rows |
Source code
|
| .resolve_filter_sources |
Source code
|
| .resolve_genome |
Source code
|
| .resolve_hub_target_col |
Source code
|
| .rm_track_dir |
Source code
|
| .sample_chroms_from_file |
Source code
|
| .save_intervals |
Source code
|
| .set_vtrack_iterator_1d |
Source code
|
| .store_chrom_aliases |
Source code
|
| .track_dir |
Source code
|
| .translate_chroms |
Source code
|
| .translate_chroms_per_row |
Source code
|
| .ucsc_fetch_assets |
Source code
|
| .validate_recipe |
Source code
|
| .validate_source_chromosomes |
Source code
|
| .vtrack_check_params_dots_collision |
Source code
|
| .vtrack_check_unknown_params |
Source code
|
| .vtrack_params_kmer |
Source code
|
| .vtrack_params_masked |
Source code
|
| .vtrack_params_neighbor_count |
Source code
|
| .vtrack_params_pwm |
Source code
|
| .vtrack_params_pwm_edit_distance |
Source code
|
| .vtrack_params_pwm_edit_distance_lse |
Source code
|
| .vtrack_params_pwm_n_mutations |
Source code
|
| .with_db_context |
Source code
|
| .with_track_context |
Source code
|
| .write_genome_info |
Source code
|
| [.intervs_mat |
Man page
|
| `%||%` |
Source code
|
| `[.intervs_mat` |
Source code
|
| calculate_optimal_gmax_data_size |
Source code
|
| format_bytes |
Source code
|
| gbins.quantiles |
Man page
Source code
|
| gbins.summary |
Man page
Source code
|
| gcis_decay |
Man page
Source code
|
| gcluster.run |
Man page
Source code
|
| gcompute_strands_autocorr |
Man page
Source code
|
| gcor |
Man page
Source code
|
| gdataset.example_path |
Man page
Source code
|
| gdataset.info |
Man page
Source code
|
| gdataset.load |
Man page
Source code
|
| gdataset.ls |
Man page
Source code
|
| gdataset.save |
Man page
Source code
|
| gdataset.unload |
Man page
Source code
|
| gdb.build_genome |
Man page
Source code
|
| gdb.convert_to_indexed |
Man page
Source code
|
| gdb.create |
Man page
Source code
|
| gdb.create_genome |
Man page
Source code
|
| gdb.create_linked |
Man page
Source code
|
| gdb.export_fasta |
Man page
Source code
|
| gdb.genome_info |
Man page
Source code
|
| gdb.get_readonly_attrs |
Man page
Source code
|
| gdb.info |
Man page
Source code
|
| gdb.init |
Man page
Source code
|
| gdb.init.examples |
Man page
|
| gdb.init_examples |
Man page
Source code
|
| gdb.install_gff3_converter |
Man page
Source code
|
| gdb.install_gtf_converter |
Man page
Source code
|
| gdb.install_intervals |
Man page
Source code
|
| gdb.list_genomes |
Man page
Source code
|
| gdb.mark_cache_dirty |
Man page
Source code
|
| gdb.reload |
Man page
Source code
|
| gdb.set_readonly_attrs |
Man page
Source code
|
| gdb.unload |
Man page
Source code
|
| gdir.cd |
Man page
Source code
|
| gdir.create |
Man page
Source code
|
| gdir.cwd |
Man page
Source code
|
| gdir.rm |
Man page
Source code
|
| gdist |
Man page
Source code
|
| get_bigWigToWig_bin |
Source code
|
| get_system_memory |
Source code
|
| gextract |
Man page
Source code
|
| gftp_download |
Source code
|
| gftp_download_glob |
Source code
|
| gftp_list |
Source code
|
| ggenome.implant |
Man page
Source code
|
| ggenome.transplant |
Man page
Source code
|
| gintervals |
Man page
Source code
|
| gintervals.2d |
Man page
Source code
|
| gintervals.2d.all |
Man page
Source code
|
| gintervals.2d.band_intersect |
Man page
Source code
|
| gintervals.2d.convert_to_indexed |
Man page
Source code
|
| gintervals.2d.intersect |
Man page
Source code
|
| gintervals.2d.union |
Man page
Source code
|
| gintervals.all |
Man page
Source code
|
| gintervals.annotate |
Man page
Source code
|
| gintervals.as_chain |
Man page
Source code
|
| gintervals.attr.export |
Man page
Source code
|
| gintervals.attr.get |
Man page
Source code
|
| gintervals.attr.import |
Man page
Source code
|
| gintervals.attr.set |
Man page
Source code
|
| gintervals.canonic |
Man page
Source code
|
| gintervals.chrom_sizes |
Man page
Source code
|
| gintervals.convert_to_indexed |
Man page
Source code
|
| gintervals.coverage_fraction |
Man page
Source code
|
| gintervals.covered_bp |
Man page
Source code
|
| gintervals.dataset |
Man page
Source code
|
| gintervals.dbs |
Man page
Source code
|
| gintervals.diff |
Man page
Source code
|
| gintervals.exists |
Man page
Source code
|
| gintervals.force_range |
Man page
Source code
|
| gintervals.from_mat |
Man page
Source code
|
| gintervals.from_strings |
Man page
Source code
|
| gintervals.import_bed |
Man page
Source code
|
| gintervals.import_genes |
Man page
Source code
|
| gintervals.import_gff |
Man page
Source code
|
| gintervals.import_vcf |
Man page
Source code
|
| gintervals.intersect |
Man page
Source code
|
| gintervals.is.bigset |
Man page
Source code
|
| gintervals.liftover |
Man page
Source code
|
| gintervals.load |
Man page
Source code
|
| gintervals.load_chain |
Man page
Source code
|
| gintervals.ls |
Man page
Source code
|
| gintervals.mapply |
Man page
Source code
|
| gintervals.mark_overlaps |
Man page
Source code
|
| gintervals.neighbors |
Man page
Source code
|
| gintervals.neighbors.directional |
Man page
Source code
|
| gintervals.neighbors.downstream |
Man page
Source code
|
| gintervals.neighbors.upstream |
Man page
Source code
|
| gintervals.normalize |
Man page
Source code
|
| gintervals.path |
Man page
Source code
|
| gintervals.quantiles |
Man page
Source code
|
| gintervals.random |
Man page
Source code
|
| gintervals.rbind |
Man page
Source code
|
| gintervals.rm |
Man page
Source code
|
| gintervals.save |
Man page
Source code
|
| gintervals.summary |
Man page
Source code
|
| gintervals.to_mat |
Man page
Source code
|
| gintervals.union |
Man page
Source code
|
| gintervals.update |
Man page
Source code
|
| giterator.cartesian_grid |
Man page
Source code
|
| giterator.intervals |
Man page
Source code
|
| glookup |
Man page
Source code
|
| gpartition |
Man page
Source code
|
| gquantiles |
Man page
Source code
|
| grevcomp |
Man page
Source code
|
| gsample |
Man page
Source code
|
| gscreen |
Man page
Source code
|
| gsegment |
Man page
Source code
|
| gseq.comp |
Man page
Source code
|
| gseq.extract |
Man page
Source code
|
| gseq.kmer |
Man page
Source code
|
| gseq.kmer.dist |
Man page
Source code
|
| gseq.pwm |
Man page
Source code
|
| gseq.pwm_edits |
Man page
Source code
|
| gseq.read_homer |
Man page
Source code
|
| gseq.read_jaspar |
Man page
Source code
|
| gseq.read_meme |
Man page
Source code
|
| gseq.rev |
Man page
Source code
|
| gseq.revcomp |
Man page
|
| gsetroot |
Man page
Source code
|
| gsummary |
Man page
Source code
|
| gsynth.bin_map |
Man page
Source code
|
| gsynth.cell_merge |
Man page
Source code
|
| gsynth.convert |
Man page
Source code
|
| gsynth.forbid_kmer |
Man page
Source code
|
| gsynth.load |
Man page
Source code
|
| gsynth.random |
Man page
Source code
|
| gsynth.replace_kmer |
Man page
Source code
|
| gsynth.sample |
Man page
Source code
|
| gsynth.save |
Man page
Source code
|
| gsynth.score |
Man page
Source code
|
| gsynth.train |
Man page
Source code
|
| gtrack.2d.convert_to_indexed |
Man page
Source code
|
| gtrack.2d.create |
Man page
Source code
|
| gtrack.2d.import |
Man page
Source code
|
| gtrack.2d.import_contacts |
Man page
Source code
|
| gtrack.array.extract |
Man page
Source code
|
| gtrack.array.get_colnames |
Man page
Source code
|
| gtrack.array.import |
Man page
Source code
|
| gtrack.array.set_colnames |
Man page
Source code
|
| gtrack.attr.export |
Man page
Source code
|
| gtrack.attr.get |
Man page
Source code
|
| gtrack.attr.import |
Man page
Source code
|
| gtrack.attr.set |
Man page
Source code
|
| gtrack.convert |
Man page
Source code
|
| gtrack.convert_to_indexed |
Man page
Source code
|
| gtrack.copy |
Man page
Source code
|
| gtrack.create |
Man page
Source code
|
| gtrack.create_dense |
Man page
Source code
|
| gtrack.create_dirs |
Man page
Source code
|
| gtrack.create_pwm_energy |
Man page
Source code
|
| gtrack.create_sparse |
Man page
Source code
|
| gtrack.dataset |
Man page
Source code
|
| gtrack.dbs |
Man page
Source code
|
| gtrack.exists |
Man page
Source code
|
| gtrack.export_bedgraph |
Man page
Source code
|
| gtrack.export_bigwig |
Man page
Source code
|
| gtrack.import |
Man page
Source code
|
| gtrack.import_mappedseq |
Man page
Source code
|
| gtrack.import_set |
Man page
Source code
|
| gtrack.info |
Man page
Source code
|
| gtrack.liftover |
Man page
Source code
|
| gtrack.lookup |
Man page
Source code
|
| gtrack.ls |
Man page
Source code
|
| gtrack.modify |
Man page
Source code
|
| gtrack.mv |
Man page
Source code
|
| gtrack.path |
Man page
Source code
|
| gtrack.rm |
Man page
Source code
|
| gtrack.smooth |
Man page
Source code
|
| gtrack.var.get |
Man page
Source code
|
| gtrack.var.ls |
Man page
Source code
|
| gtrack.var.rm |
Man page
Source code
|
| gtrack.var.set |
Man page
Source code
|
| gvtrack.array.slice |
Man page
Source code
|
| gvtrack.clear |
Man page
Source code
|
| gvtrack.create |
Man page
Source code
|
| gvtrack.filter |
Man page
Source code
|
| gvtrack.info |
Man page
Source code
|
| gvtrack.iterator |
Man page
Source code
|
| gvtrack.iterator.2d |
Man page
Source code
|
| gvtrack.ls |
Man page
Source code
|
| gvtrack.rm |
Man page
Source code
|
| gwget |
Man page
Source code
|
| gwilcox |
Man page
Source code
|
| misha |
Man page
|
| misha-NaN |
Man page
|
| misha-package |
Man page
|
| print.gsynth.model |
Man page
Source code
|
| rbind.intervs_mat |
Man page
Source code
|
| repair_names |
Source code
|
| rescue_ALLGENOME |
Source code
|
